are the wheel nuts tight ? mine does not clunk, I can't think what
might clunk in a gear box. They are not particularly amazing gear boxes
in general if you ask me... IANAM BTW !

Dave,

Just came across your post. My yr 2000 Focus 1.8 manual has pretty
much the same noise as what you've described. It only came about after
I had the clutch kit changed - it certainly didn't have the clonking
noise before that. Sound comes on during clutch let up during
changes,noticeable only in 1st and 2nd, on progressive acceleration.
There's no sound when you stand on the gas and work the stick.

I suspect that the mounting of something within the assy may not now
be entirely kosher. There's a little bit of judder as you inch along,
slipping the clutch slightly (as when adjusting during parking); might
be that the renewal didn't align things properly.

The local Ford SC (here in Malaysia) say the sound's coming from a
worn steering rack tie-end. Which is rubbish, because I had them
changed before the new clutch kit went in.

Doesn't really affect anything in terms of drivability aspects, but it
does get a little irritating sometimes. Short of having them drop the
box again (and God knows what else they'll get wrong if they manage to
rectify things), I've learnt to live with it.

Glad to hear in your case, you're plugging a replacement.